Similar problem here, May 16 invoice looked good but fees since the 16th where higher than the whole month! Used the new payPal form, and ended up paying the whole amount (the new one sucks). Emailed asking what the fees where for - no response on that one to date - but lo, and behold, a credit shows up!
Emailed asking what happened, and now three times, they tell me I overpaid! No mention of the extra fees - nothing. One email said refunds only in a credit position (at that point I had a zero balance 'cause they hadn't corrected it yet), and now no one will respond to the refund question (four emails to eBay, and going strong!) Weird and frustrating and not good!